Hi Justin, Thanks for suggestion...and pointing out that there is problem with topology ...now i checked ligand file..there hydrogens were not added correctly..so swissparam tool was not correct topology .. now i corrected it ..it works perfectly ..
Thanks a lot Sainitin On Tue, Jul 16, 2013 at 5:05 PM, Sainitin Donakonda <saigr...@gmail.com>wrote: > Hi all, > > I have 3 protein-drug complexes (same protein and different drugs) i > performed 20 ns molecular dynamics simulation..using same parameters (i > mean energy minimzation parameters) ..2 of them was successful for MD > simulation..(im using Charmm 27 Force field) > > But 1 drug protein complex is failed in Energy minimization step itself.. > showing following error > > *Error : whole protein drug complex > * > * > * > *708 particles communicated to PME node 2 are more than 2/3 times the > cut-off out of the domain decomposition cell of their charge group in > dimension x.* > *This usually means that your system is not well equilibrated > > * > Then i looked up > http://www.gromacs.org/Documentation/Terminology/Blowing_Up > > In this i followed up suggestions which are mentioned in diagnosing > unstable system as follows. > > First i did energy minimization for protein alone which worked perfectly > with out any error. > > Second i did energy minimization for ligand alone (with out protein)..this > showed again following error.. > > Error 2 : Ligand only > > Fatal error: > *184 particles communicated to PME node 2 are more than 2/3 times the > cut-off out of the domain decomposition cell of their charge group in > dimension x. > This usually means that your system is not well equilibrated.* > > So there is problem with small molecule...not with the protein ..here i > think i should tune parameters in .MDP file..which i m just not getting how > to do.. > > here is the EM.mdp file.. > > ; LINES STARTING WITH ';' ARE COMMENTS > title = Minimization ; Title of run > define = -DFLEX_TI3P ; defines to pass to the > preprocessor > constraints = none > > ; 7.3.3 Run Control > integrator = steep ; steepest descents energy > minimization > nsteps = 2000 ; maximum number of steps to > integrate > energygrps = LIG ; group(s) to write to energy file > > ; 7.3.5 Energy Minimization > emtol = 1000 ; [kJ/mol/nm] minimization is > converged when max force is < emtol > emstep = 0.01 ; [nm] initial step-size > dt = 0.01 > > > ; 7.3.9 Neighbor Searching > nstlist = 1 ; [steps] freq to update neighbor > list > nstxout = 1 > ns_type = grid ; method of updating neighbor list > pbc = xyz ; periodic boundary conditions in > all directions > rlist = 1.2 ; [nm] cut-off distance for the > short-range neighbor list > rlistlong = 1.4 ; [nm] Cut-off distance from the > long-range neighbor list > > ; 7.3.10 Electrostatics > coulombtype = PME ; Particle-Mesh Ewald > electrostatics > rcoulomb = 1.2 ; [nm] distance for Coulomb cut-off > > ; 7.3.11 VdW > vdwtype = switch ; twin-range cut-off with rlist > where rvdw >= rlist > rvdw = 1.2 ; [nm] distance for LJ cut-off > rvdw_switch = 0.2 ; Start switching th LJ potential > DispCorr = Ener ; apply long range dispersion > corrections for energy > > ; 7.3.13 Ewald > fourierspacing = 0.12 ; [nm] grid spacing for FFT grid > when using PME > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > pme_order = 4 ; interpolation order for PME, 4 = > cubic > ewald_rtol = 1e-5 ; relative strength of > Ewald-shifted potential at rcoulomb > optimize_fft = yes > > > Can any body please tell me how to optimize these parameters > > Thanks, > Nitin > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists